טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentGolan Lagziel Tal
SubjectUnraveling the Regulatory Elements and Factors for Gene
Expression in Cardiac Fibroblasts and
Cardiomyocytes
DepartmentDepartment of Medicine
Supervisor ASSOCIATE PROF. Izhak Kehat
Full Thesis textFull thesis text - English Version


Abstract

Gene transcription, the first step of gene expression, is controlled by cis-regulatory genomic elements (CREs), e.g. promoters and enhancers; while the promoter is just next to the gene, the enhancers occur thousands of base-pairs far from it. Transcriptional control involves the establishment of physical connections among genes and those regulatory elements. Furthermore, it is known that activation of enhancers is controlled by specific tissue transcription factors (TFs) that bind them in specific binding sites; single enhancer can bind multiple transcription factors. This fact implies that enhancers, and other regulatory elements, are located in ‘open’ chromatin regions, between adjacent nucleosomes, which allows enhancer-transcription factors interaction. There are two models for enhancer activity: ‘enhanceosome’ model and ‘billboard’ model; while the former requires rigid transcription factors binding sites organization within the enhancer, the latter doesn’t.

Cardiac fibroblasts play key roles in both health and disease and they represent a non-negligible cell population in the heart tissue. Unlike cardiomyocytes, the regulatory elements, transcription factors, and mechanisms of expression control of cardiac fibroblasts have not been fully elucidated. Our objectives were to identify the CREs that regulate cardiac fibroblasts specific genes transcription, and to understand the mechanisms and principles behind their function. To do so, we used a differential open chromatin approach, coupled with active enhancer mark, transcriptomic, and computational TFs binding analysis to map cell-type-specific active enhancers in cardiac fibroblasts and cardiomyocytes, and outline the TFs families that control them. In our analysis, as been done in previous studies, enhancers were defined as open genomic regions enriched with specific histone acetylation as a mark for active enhancer. This approach was validated by its ability to uncover the known cardiomyocyte TF biology in an unbiased manner, and was then applied to cardiac fibroblasts. We identified Tead, Sox9, Smad, Tcf, Meis, Rbpj, and Runx1 as the main cardiac fibroblasts TF families. Our analysis shows that in both cell types, distal enhancers, containing concentrated combinatorial clusters of multiple tissue expressed TFs recognition motifs, are combinatorically clustered around tissue specific genes, while common enhancers to both cell types, are clustered around housekeeping genes. This model for tissue specific gene expression in the heart supports the general ‘billboard’ model for enhancer organization.